Hi Dong,
Apache seems to be unhappy :) the user directive you have added to
httpd.conf does not have the right permissions on the biomart-perl/
directory. A good test would be to
chmod -R 775 biomart-perl
and see if that fixes the problem.
Good luck!
Syed
> Hi Syed,
>
> Thank you very much!! this problem seems solved, however, there is another
> problem showing up, could you help me again? error_log says:
>
> [error] Error in processing template error.tt: file error - cache failed
> to write error.ttc: Error in tempfile() using /var/www/ht
> ml/biomart-perl/conf/templates/default/XXXXXXXXXX: Parent directory
> (/var/www/html/biomart-perl/conf/templates/default/) is not writable\n at
> /usr/lib/perl5/
> site_perl/5.8.8/i386-linux-thread-multi/Template/Document.pm line
> 295\n\n\nTrace begun at /var/www/html/biomart-perl/lib/BioMart/Web.pm line
> 267\nBioMart::We
> b::process_template('BioMart::Web=HASH(0x81ec2e0c)', 'error.tt',
> 'HASH(0x84383194)') called at /var/www/html/biomart-perl/cgi-bin/martview
> line 122\nModPerl:
> :ROOT::ModPerl::Registry::var_www_html_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x8421355c)')
> called at /usr/lib/perl5/vendor_p
> erl/5.8.8/i386-linux-thread-multi/ModPerl/RegistryCooker.pm line 203\neval
> {...} at
> /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/ModPerl/Registry
> Cooker.pm line
> 203\nModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x84213610)')
> called at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Mod
> Perl/RegistryCooker.pm line
> 169\nModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x84213610)')
> called at /usr/lib/perl5/vendor_perl/5.8.8/i3
> 86-linux-thread-multi/ModPerl/Registry.pm line
> 30\nModPerl::Registry::handler('ModPerl::Registry',
> 'Apache2::RequestRec=SCALAR(0x8421355c)') called at -e lin
> e 0\neval {...} at -e line 0\n
>
> Dong
>
>> Hi Dong,
>>
>> the --clean option is a perl bin/configure.pl switch e.g
>> perl bin/configure.pl -r conf/your_reg.xml --clean
>> see docs for details.
>>
>> it seems that your httpd.conf needs a apache user directive, the user
>> who has rights to start/stop apache. please manually add this to
>> conf/httpd.conf and then start your apache. This is most likely the
>> case.
>>
>> cheers
>> Syed
>>
>>
>> [email protected] wrote:
>>> Hi Richard,
>>>
>>> could you let me know how to use --clean option in detail? I checked
>>> the
>>> error_log which says:
>>>
>>> [warn] pid file /var/www/html/biomart-perl/logs/httpd.pid overwritten
>>> --
>>> Unclean shutdown of previous Apache run?
>>> [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user
>>> name
>>> from uid 4294967295, you probably need to modify the User directive
>>> [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user
>>> name
>>> from uid 4294967295, you probably need to modify the User directive
>>> [Tue Jan 13 15:55:44 2009] [notice] Apache/2.2.6 (Unix) mod_perl/2.0.2
>>> Perl/v5.8.8 configured -- resuming normal operations
>>> [Tue Jan 13 15:55:44 2009] [alert] Child 24664 returned a Fatal
>>> error...
>>> Apache is exiting!
>>>
>>> do you have any idea from this information?
>>>
>>> Thanks!
>>>
>>> Dong
>>>
>>>
>>>
>>>
>>>
>>>> Also it might be worth checking the contents of the conf/httpd.conf
>>>> file
>>>> to see if it has correctly populated it with the correct port numbers
>>>> etc.
>>>>
>>>> If it hasn't, rerun bin/configure.pl with the --clean option to force
>>>> it
>>>> to regenerate httpd.conf properly.
>>>>
>>>> cheers,
>>>> Richard
>>>>
>>>> [email protected] wrote:
>>>>
>>>>> Hi Syed,
>>>>>
>>>>> Actually, the host name 'mandolin.caltech.edu' is already in the
>>>>> /etc/hosts file and the web server works well. I follow your
>>>>> suggestion
>>>>> to
>>>>> try 127.0.0.1, the same trouble happened. could you give me other
>>>>> suggestion?
>>>>> Thank you!
>>>>>
>>>>> Dong
>>>>>
>>>>>
>>>>>
>>>>>> Hi Dong,
>>>>>>
>>>>>> your apache startup error says it all, the apache server doesnt
>>>>>> recognise your host name (the one which you are specifying in
>>>>>> settings.conf). You need to modify the /etc/hosts file on your
>>>>>> system
>>>>>> and then restart apache server. Once done, reconfigure BioMart (only
>>>>>> perl bin/configure.pl....) and restart your apache. A good test
>>>>>> would
>>>>>> be to put 127.0.0.1 in settings.conf and configure Biomart, restart
>>>>>> apache and see if you can access the webserver on
>>>>>> http://127.0.0.1:5430/biomart/martview
>>>>>>
>>>>>> Stepwise solution can be seen here:
>>>>>>
>>>>>> http://digitaldeviation.com/articles/apache-articles/apache-error-could-not-reliably-determine-servers-fully-qualified-domain-na
>>>>>>
>>>>>> Good Luck!,
>>>>>> Syed
>>>>>>
>>>>>>
>>>>>>
>>>>>> [email protected] wrote:
>>>>>>
>>>>>>> Hi Syed,
>>>>>>>
>>>>>>> here is the output after configure:
>>>>>>>
>>>>>>> # perl bin/configure.pl -r conf/spbase_annotation1022_6.xml
>>>>>>>
>>>>>>> Do you want to install in API only mode [y/n] [n]: n
>>>>>>>
>>>>>>> Checking prerequisites ...[Looks good]
>>>>>>>
>>>>>>> APACHE: /usr/sbin/httpd
>>>>>>> HOST: http://mandolin.caltech.edu
>>>>>>> PORT: 5430
>>>>>>> PROXY:
>>>>>>> LOCATION: biomart
>>>>>>>
>>>>>>> You can change the above configuration by editing
>>>>>>> "biomart-perl/conf/settings.conf"
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
>>>>>>> configuration
>>>>>>> Have Apache DSO-support and ModPerl library file present,
>>>>>>> configuring
>>>>>>> ModPerl in httpd.conf.
>>>>>>> Libdir /var/www/html/biomart-perl/lib is not in @INC, adding to
>>>>>>> @INC
>>>>>>>
>>>>>>> Processing Cached Registry:
>>>>>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached
>>>>>>>
>>>>>>> # /usr/sbin/httpd -d $PWD -f $PWD/conf/httpd.conf
>>>>>>>
>>>>>>> Processing Cached Registry:
>>>>>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached
>>>>>>>
>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>> line
>>>>>>> 131.
>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>> line
>>>>>>> 139.
>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>> line
>>>>>>> 158.
>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>> line
>>>>>>> 169.
>>>>>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in
>>>>>>> line
>>>>>>> 185.
>>>>>>> httpd: Could not reliably determine the server's fully qualified
>>>>>>> domain
>>>>>>> name, using mandolin.caltech.edu for ServerName
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>> attached are the httpd.conf and settings.conf.
>>>>>>>
>>>>>>> Thank you very much for your help!
>>>>>>>
>>>>>>> Dong
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi Dong,
>>>>>>>>
>>>>>>>> please send me the following:
>>>>>>>>
>>>>>>>> - conf/httpd.conf
>>>>>>>> - on screen output when you run perl bin/configure.pl......
>>>>>>>> - conf/settings.conf
>>>>>>>>
>>>>>>>>
>>>>>>>> thanks
>>>>>>>> Syed
>>>>>>>>
>>>>>>>>
>>>>>>>> [email protected] wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Friends:
>>>>>>>>>
>>>>>>>>> I successfully set up a mart in one of my machines, then, I moved
>>>>>>>>> whole
>>>>>>>>> mart database into another machine, and the configuring ("perl
>>>>>>>>> bin/configure.pl -r conf/annotation1022_6.xml", "/usr/sbin/httpd
>>>>>>>>> -d
>>>>>>>>> $PWD
>>>>>>>>> -f $PWD/conf/httpd.conf")seems work, however, when point web
>>>>>>>>> browser
>>>>>>>>> to
>>>>>>>>> the corresponding URL, I got a error: "Firefox can't establish a
>>>>>>>>> connection to the server at mandolin.caltech.edu:5430." does this
>>>>>>>>> mean
>>>>>>>>> mart is not portable? do I have to build mart at each machine
>>>>>>>>> separately?
>>>>>>>>> or I missed some httpd configuration?
>>>>>>>>> Thanks!
>>>>>>>>>
>>>>>>>>> Dong
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>
>>>>>
>>>> --
>>>> Richard Holland, BSc MBCS
>>>> Finance Director, Eagle Genomics Ltd
>>>> M: +44 7500 438846 | E: [email protected]
>>>> http://www.eaglegenomics.com/
>>>>
>>>>
>>>
>>>
>>
>
>
>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
